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Report date: 2020-07-27

Top Level Haplogroup Markers

All markers shown, except those in parentheses, are present at ≥80% in the top level haplogroups of the current Mitomap dataset. Parentheses indicate variants which are ≥50% but <80%. Lowercase letters indicate transversions (e.g., 3516a). Markers matching the rCRS reference value are indicated with "=" (e.g., 263A=); while these latter markers are important to delineate the haplogroup in the phylogenetic tree, they will not usually be listed in genetic test reports because they are identical to the reference rCRS sequence. There are twelve high frequency ancestral variants in this table that are extremely common across all lineages and, as such, are not generally informative for haplotyping. Conversely, the lack of one or more of these variants may be more of use. These variants are 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, & 16519C. For lineage distribution, see https://www.mitomap.org/MITOMAP/TopVariants.

For clinicians and researchers assessing variant pathogenicity: all Ancestral Markers on this page satisfy ClinGen’s BA1 (benign standalone) frequency criteria for mtDNA variants. All haplogroup (HG) markers shown on this page qualify at BA1 for a patient who is a member of the same haplogroup. For a full list of variants satisfying BA1 or BS1 (benign supporting) on a global frequency level, see ClinGenApproved.

NEW For markers found at the letter-number-letter haplogroup level click here.

Lineage Top Level Haplogroup # Seqs Ancestral Marker Motif
(the " RSRS50")
HG Markers Other Selected Markers
LL01701247A, 750G, 769A, 825A, 1018A, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16187T, 16189C, 16223T, 16230G, 16311C

(73G, 146C, 152C, 195C, 1438G, 2706G, 16129A, 16519C)
1048T, 3516a, 5442C, 6185C, 9042T, 9347G, 9755A, 10589A, 12007A, 12720G

(514d, 4586C, 9818T, 16172C)
(263A=)
LL187973G, 152C, 195C, 247A, 263G, 750G, 769A, 825A, 1018A, 2706G, 2758A, 2885C, 3594T, 4104G, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13105G, 13506T, 13650T, 14766T, 15326G, 16187T, 16189C, 16223T, 16278T, 16311C, 16519C

(1438G, 16129A)
182T, 3666A, 7055G, 7389C, 13789C, 14178C, 14560A

(151T, 186a, 189c, 316A, 514d, 2394d, 5951G, 6071C, 8027A, 9072G, 10321C, 10586A, 12810G, 13485G, 14000A, 14911T, 16294T, 16360T)
LL2132973G, 146C, 152C, 195C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T

(11914A)
2416C, 8206A, 9221G, 10115C, 11944C, 13590A, 15301A, 16390A

(2789T, 7175C, 7274T, 7771G, 12693G, 13803G, 14566G, 15784C, 16294T, 16309G)
150C=, 16311T=
LL3214173G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
15301A

(150T)
3594C=, 769G=, 1018G=, 16311T=
LL411073G, 263G, 750G, 769A, 1018A, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T, 16311C

(146C, 16519C)
3918A, 15301A, 16362C

(244G, 315CC, 1413C, 8104C, 9855G, 12609C, 13470G, 16293T, 16355T, 16399G)
3594C=, L4b2: 146C
LL53973G, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13506T, 13650T, 14766T, 15326G, 16129A, 16223T, 16278T, 16311C

(152C, 195C, 13105G, 16189C)
182T, 3423C, 5147A, 7972G, 12432T, 12950G, 14581C, 16148T, 16166G

(514d, 709A, 851G, 1822C, 5111T, 5656G, 6182A, 6297C, 7424G, 8155A, 8188G, 8582T, 9305A, 9329A, 11025C, 11881T, 12236A, 13722G, 14212C, 14239T, 14905A, 14971C, 15217A, 15884A, 16355T, 16362C)
Length variants in the 455-459 region [459CCsor 455TTC or 455TTTC].
LL61273G, 146C, 152C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4769G, 7028T, 7256T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T, 16311C, 16519C182T, 185C, 709A, 770T, 961C, 1461G, 4964T, 5267C, 6002G, 6284G, 9332T, 10978G, 11116C, 11743T, 12771A, 13710G, 14791T, 14959G, 15244G, 15289C, 15301A, 15499T, 16048A, 16224C

(265C, 309CCT, 310C)
MC179073G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 11914A, 12705T, 14766T, 15326G, 16223T

(16519C)
248d, 489C, 3552A, 4715G, 7196a, 8584A, 9545G, 10400T, 13263G, 14318C, 14783C, 15043A, 15301A, 15487T, 16298C, 16327T
MD239173G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T489C, 3010A, 4883T, 5178a, 8414T, 10400T, 14668T, 14783C, 15043A, 15301A, 16362C
ME45973G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 15326G, 16223T, 16519C489C, 3027C, 3705A, 4248C, 4491A, 7598A, 10400T, 10834T, 13254C, 13626T, 14577C, 14783C, 15043A, 15301A, 16362C, 16390A

(6620C, 16291T)
MG44873G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T489C, 709A, 4833G, 5108C, 10400T, 14569A, 14783C, 15043A, 15301A, 16362C

(5601T, 9575A, 13563G)
MM531173G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
489C, 10400T, 14783C, 15043A, 15301A
MQ27373G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16129A, 16311C

(146C, 16223T)
489C, 4117C, 5460A, 5843G, 8790A, 10400T, 12940A, 13500C, 14783C, 15043A, 15301A, 16241G

(89C, 92A, 8964T, 14025C, 16144C, 16148T, 16265c, 16343G)
MZ20573G, 152C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
248d, 489C, 4715G, 6752G, 7196a, 8584A, 9090C, 10400T, 14783C, 15043A, 15301A, 15487T, 15784C, 16185T, 16260T, 16298C

(151T)
NA139573G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(146C)
235G, 514d, 663G, 1736G, 4248C, 4824G, 8794T, 16290T, 16319A, 16362C

(153G, 310C, 8027A, 12007A, 16111T)
NB426173G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16189C, 16519C

(146C)
16183c, 16217C

(16182c, 16261T)
Branches B4 and B9: 10398A=,s8271 9bp deletions [8271_8279del or 8281_8289del];
Branch B4: 514_515delCA
Branch B5: 146T=, 16217T=
NF169573G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G

(16129A, 16519C)
248d, 3970T, 6392C, 10310A, 13928C, 16304C

(514d, 6962A, 9053A, 10609C, 12406A, 12882T, 13759A, 16172C)
NH9724263G, 750G, 1438G, 4769G, 8860G, 15326G

(16519C)
2706A=, 7028C=
NHV791263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G(310C)14766C=
NI75373G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G, 16129A, 16223T, 16519C199C, 204C, 250C, 1719A, 4529T, 8251A, 10034C, 10238C, 12501A, 13780G, 15043A, 15924G, 16391A
NJ246973G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G295T, 489C, 4216C, 11251G, 12612G, 13708A, 15452a, 16069T, 16126C

(462T, 3010A, 14798C)
NK192573G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G, 16311C, 16519C1189C, 1811G, 3480G, 9055A, 9698C, 10550G, 11299C, 11467G, 12308G, 12372A, 14167T, 14798C, 16224C

(315CC, 497T)
NN82673G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
8701A=, 9540T=, 10398A=, 10400C=, 10873T=, 15301G=
NO873G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(152C, 16189C, 16519C)
6755A, 9140T, 16213A

(794C, 5563A, 16183c)
NP25573G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G15607G

(6077T, 10118C)
NR1132263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 14766T, 15326G

(73G, 11719A, 16519C)
12705C=, 16223C=
NS4973G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G

(152C, 16223T)
8404C
NT234973G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16519C709A, 1888A, 4216C, 4917G, 8697A, 10463C, 11251G, 13368A, 14905A, 15452a, 15607G, 15928A, 16126C, 16294T

(11812G, 14233G)
10398A=
NU452973G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G11467G, 12308G, 12372A
NV728263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G72C, 4580A, 15904T, 16298C

(310C)
NW57773G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T, 16519C189G, 204C, 207A, 709A, 1243C, 3505G, 5046A, 5460A, 8251A, 8994A, 11674T, 11947G, 12414C, 15884C, 16292T

(194T)
NX49773G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16189C, 16223T, 16278T, 16519C1719A, 6221C, 6371T, 13966G, 14470C

(153G, 225A, 16183c)
NY14173G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G

(146C, 16519C)
5417A, 8392A, 14178C, 14693G, 16126C, 16231C

(3834A, 7933G)
16223C=

Ancestral SNPs are spread throughout the human mtDNA tree. These ancestral variants, the "RSRS50", are: 73G, 146C, 152C, 195C, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16129A, 16187T, 16189C, 16223T, 16230G, 16278T, 16311C, 16519C. The most widespread across all lineages are shown in bold.

Additionally, the RSRS ancestor sequence has two single base deletions, 523d & 524d, which are located at the end of a string of CA repeats. Indels in this region are variously notated and common. These two deleted bases are not indexed in Mitomap's "RSRS50" set and are among those variants specifically excluded by Phylotree in the construction of their master tree.

Topic revision: r29 - 27 Jul 2020, UnknownUser

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